{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,12]],"date-time":"2026-11-12T11:01:56Z","timestamp":1794481316747,"version":"4.9.1"},"publisher-location":"New York, NY","reference-count":37,"publisher":"Springer New York","isbn-type":[{"value":"9781493911141","type":"print"},{"value":"9781493911158","type":"electronic"}],"license":[{"start":{"date-parts":[[2014,1,1]],"date-time":"2014-01-01T00:00:00Z","timestamp":1388534400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2014,1,1]],"date-time":"2014-01-01T00:00:00Z","timestamp":1388534400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014]]},"DOI":"10.1007\/978-1-4939-1115-8_20","type":"book-chapter","created":{"date-parts":[[2014,7,21]],"date-time":"2014-07-21T09:41:47Z","timestamp":1405935707000},"page":"365-374","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Computational Antigenic Epitope Prediction by Calculating Electrostatic Desolvation Penalties of Protein Surfaces"],"prefix":"10.1007","author":[{"given":"S\u00e9bastien","family":"Fiorucci","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Zacharias","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,6,27]]},"reference":[{"issue":"6","key":"20_CR1","doi-asserted-by":"publisher","first-page":"3824","DOI":"10.1073\/pnas.78.6.3824","volume":"78","author":"TP Hopp","year":"1981","unstructured":"Hopp TP, Woods KR (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A 78(6): 3824\u20133828","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"19","key":"20_CR2","doi-asserted-by":"publisher","first-page":"5425","DOI":"10.1021\/bi00367a013","volume":"25","author":"JM Parker","year":"1986","unstructured":"Parker JM, Guo D, Hodges RS (1986) New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry 25(19):5425\u20135432","journal-title":"Biochemistry"},{"issue":"3","key":"20_CR3","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1128\/jvi.55.3.836-839.1985","volume":"55","author":"EA Emini","year":"1985","unstructured":"Emini EA, Hughes JV, Perlow DS, Boger J (1985) Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol 55(3):836\u2013839","journal-title":"J Virol"},{"issue":"4","key":"20_CR4","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1002\/jmr.893","volume":"21","author":"Y El-Manzalawy","year":"2008","unstructured":"El-Manzalawy Y, Dobbs D, Honavar V (2008) Predicting linear B-cell epitopes using string kernels. J Mol Recognit 21(4):243\u2013255","journal-title":"J Mol Recognit"},{"issue":"3","key":"20_CR5","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1007\/s00726-006-0485-9","volume":"33","author":"J Chen","year":"2007","unstructured":"Chen J, Liu H, Yang J, Chou KC (2007) Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids 33(3): 423\u2013428","journal-title":"Amino Acids"},{"issue":"1","key":"20_CR6","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1002\/prot.21078","volume":"65","author":"S Saha","year":"2006","unstructured":"Saha S, Raghava GP (2006) Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins 65(1):40\u201348","journal-title":"Proteins"},{"key":"20_CR7","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1186\/1745-7580-2-2","volume":"2","author":"JE Larsen","year":"2006","unstructured":"Larsen JE, Lund O, Nielsen M (2006) Improved method for predicting linear B-cell epitopes. Immunome Res 2:2","journal-title":"Immunome Res"},{"issue":"1","key":"20_CR8","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1110\/ps.041059505","volume":"14","author":"MJ Blythe","year":"2005","unstructured":"Blythe MJ, Flower DR (2005) Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci 14(1): 246\u2013248","journal-title":"Protein Sci"},{"issue":"2","key":"20_CR9","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1002\/jmr.815","volume":"20","author":"JA Greenbaum","year":"2007","unstructured":"Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, Mumey B, Ofran Y, Pellequer JL, Pinilla C, Ponomarenko JV, Raghava GP, van Regenmortel MH, Roggen EL, Sette A, Schlessinger A, Sollner J, Zand M, Peters B (2007) Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit 20(2):75\u201382","journal-title":"J Mol Recognit"},{"key":"20_CR10","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1186\/1471-2105-12-341","volume":"12","author":"W Zhang","year":"2011","unstructured":"Zhang W, Xiong Y, Zhao M, Zou H, Ye X, Liu J (2011) Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature. BMC Bioinformatics 12:341","journal-title":"BMC Bioinformatics"},{"key":"20_CR11","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1186\/1471-2105-11-381","volume":"11","author":"S Liang","year":"2010","unstructured":"Liang S, Zheng D, Standley DM, Yao B, Zacharias M, Zhang C (2010) EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinformatics 11:381","journal-title":"BMC Bioinformatics"},{"key":"20_CR12","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1186\/1471-2105-10-302","volume":"10","author":"S Liang","year":"2009","unstructured":"Liang S, Zheng D, Zhang C, Zacharias M (2009) Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinformatics 10:302","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"20_CR13","doi-asserted-by":"publisher","first-page":"840","DOI":"10.1016\/j.molimm.2008.09.009","volume":"46","author":"ND Rubinstein","year":"2009","unstructured":"Rubinstein ND, Mayrose I, Pupko T (2009) A machine-learning approach for predicting B-cell epitopes. Mol Immunol 46(5):840\u2013847","journal-title":"Mol Immunol"},{"issue":"Web Server issu","key":"20_CR14","doi-asserted-by":"publisher","first-page":"W612","DOI":"10.1093\/nar\/gkp417","volume":"37","author":"J Sun","year":"2009","unstructured":"Sun J, Wu D, Xu T, Wang X, Xu X, Tao L, Li YX, Cao ZW (2009) SEPPA: a computational server for spatial epitope prediction of protein antigens. Nucleic Acids Res 37(Web Server issue):W612\u2013W616","journal-title":"Nucleic Acids Res"},{"key":"20_CR15","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1186\/1471-2105-9-514","volume":"9","author":"J Ponomarenko","year":"2008","unstructured":"Ponomarenko J, Bui HH, Li W, Fusseder N, Bourne PE, Sette A, Peters B (2008) ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 9:514","journal-title":"BMC Bioinformatics"},{"issue":"12","key":"20_CR16","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1093\/bioinformatics\/btn199","volume":"24","author":"MJ Sweredoski","year":"2008","unstructured":"Sweredoski MJ, Baldi P (2008) PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics 24(12): 1459\u20131460","journal-title":"Bioinformatics"},{"issue":"11","key":"20_CR17","doi-asserted-by":"publisher","first-page":"2558","DOI":"10.1110\/ps.062405906","volume":"15","author":"P Haste Andersen","year":"2006","unstructured":"Haste Andersen P, Nielsen M, Lund O (2006) Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci 15(11):2558\u20132567","journal-title":"Protein Sci"},{"issue":"4","key":"20_CR18","doi-asserted-by":"publisher","first-page":"e62249","DOI":"10.1371\/journal.pone.0062249","volume":"8","author":"B Yao","year":"2013","unstructured":"Yao B, Zheng D, Liang S, Zhang C (2013) Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods. PLoS One 8(4):e62249","journal-title":"PLoS One"},{"issue":"9","key":"20_CR19","doi-asserted-by":"publisher","first-page":"1921","DOI":"10.1016\/j.bpj.2009.12.4332","volume":"98","author":"S Fiorucci","year":"2010","unstructured":"Fiorucci S, Zacharias M (2010) Prediction of protein\u2013protein interaction sites using electrostatic desolvation profiles. Biophys J 98(9): 1921\u20131930","journal-title":"Biophys J"},{"issue":"39","key":"20_CR20","doi-asserted-by":"publisher","first-page":"30126","DOI":"10.1074\/jbc.M110.118513","volume":"285","author":"M Soriani","year":"2010","unstructured":"Soriani M, Petit P, Grifantini R, Petracca R, Gancitano G, Frigimelica E, Nardelli F, Garcia C, Spinelli S, Scarabelli G, Fiorucci S, Affentranger R, Ferrer-Navarro M, Zacharias M, Colombo G, Vuillard L, Daura X, Grandi G (2010) Exploiting antigenic diversity for vaccine design: the chlamydia ArtJ paradigm. J Biol Chem 285(39):30126\u201330138","journal-title":"J Biol Chem"},{"key":"20_CR21","doi-asserted-by":"crossref","first-page":"5.6.1","DOI":"10.1002\/0471250953.bi0506s15","volume":"15","author":"N Eswar","year":"2006","unstructured":"Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A (2006) Comparative protein structure modeling using modeller. Curr Protoc Bioinformatics 15:5.6.1\u20135.6.30","journal-title":"Curr Protoc Bioinformatics"},{"key":"20_CR22","doi-asserted-by":"publisher","first-page":"D387","DOI":"10.1093\/nar\/gkn750","volume":"37","author":"F Kiefer","year":"2009","unstructured":"Kiefer F, Arnold K, Kunzli M, Bordoli L, Schwede T (2009) The SWISS-MODEL repository and associated resources. Nucleic Acids Res 37:D387\u2013D392","journal-title":"Nucleic Acids Res"},{"issue":"Suppl 9","key":"20_CR23","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1002\/prot.22540","volume":"77","author":"S Raman","year":"2009","unstructured":"Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, Baker D (2009) Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins 77(Suppl 9):89\u201399","journal-title":"Proteins"},{"issue":"4","key":"20_CR24","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1038\/nprot.2010.5","volume":"5","author":"A Roy","year":"2010","unstructured":"Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5(4):725\u2013738","journal-title":"Nat Protoc"},{"key":"20_CR25","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/1472-6807-11-6","volume":"11","author":"M Rostkowski","year":"2011","unstructured":"Rostkowski M, Olsson MH, Sondergaard CR, Jensen JH (2011) Graphical analysis of pH-dependent properties of proteins predicted using PROPKA. BMC Struct Biol 11:6","journal-title":"BMC Struct Biol"},{"issue":"Web Server issu","key":"20_CR26","doi-asserted-by":"publisher","first-page":"W537","DOI":"10.1093\/nar\/gks375","volume":"40","author":"R Anandakrishnan","year":"2012","unstructured":"Anandakrishnan R, Aguilar B, Onufriev AV (2012) H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res 40(Web Server issue): W537\u2013W541","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"20_CR27","doi-asserted-by":"publisher","first-page":"10037","DOI":"10.1073\/pnas.181342398","volume":"98","author":"NA Baker","year":"2001","unstructured":"Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98(18): 10037\u201310041","journal-title":"Proc Natl Acad Sci U S A"},{"key":"20_CR28","volume-title":"AMBER 12","author":"DA Case","year":"2012","unstructured":"Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Hayik S, Roitberg A, Seabra G, Swails J, Goetz AW, Kolossv\u00e1ry I, Wong KF, Paesani F, Vanicek J, Wolf RM, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh M-J, Cui G, Roe DR, Mathews DH, Seetin MG, Salomon-Ferrer R, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman PA (2012) AMBER 12. University of California, San Francisco, CA"},{"issue":"10","key":"20_CR29","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1002\/jcc.21287","volume":"30","author":"BR Brooks","year":"2009","unstructured":"Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30(10):1545\u20131614","journal-title":"J Comput Chem"},{"issue":"16","key":"20_CR30","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.1002\/jcc.20289","volume":"26","author":"JC Phillips","year":"2005","unstructured":"Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):1781\u20131802","journal-title":"J Comput Chem"},{"issue":"7","key":"20_CR31","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1093\/bioinformatics\/btt055","volume":"29","author":"S Pronk","year":"2013","unstructured":"Pronk S, Pall S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29(7):845\u2013854","journal-title":"Bioinformatics"},{"issue":"3","key":"20_CR32","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1016\/j.jsb.2012.09.010","volume":"180","author":"S Schneider","year":"2012","unstructured":"Schneider S, Zacharias M (2012) Combining geometric pocket detection and desolvation properties to detect putative ligand binding sites on proteins. J Struct Biol 180(3): 546\u2013550","journal-title":"J Struct Biol"},{"issue":"Web Server issu","key":"20_CR33","doi-asserted-by":"publisher","first-page":"W522","DOI":"10.1093\/nar\/gkm276","volume":"35","author":"TJ Dolinsky","year":"2007","unstructured":"Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35(Web Server issue): W522\u2013W525","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"20_CR34","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1016\/j.jmgm.2003.12.005","volume":"22","author":"M Feig","year":"2004","unstructured":"Feig M, Karanicolas J, Brooks CL 3rd (2004) MMTSB tool set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 22(5): 377\u2013395","journal-title":"J Mol Graph Model"},{"issue":"7","key":"20_CR35","doi-asserted-by":"publisher","first-page":"1978","DOI":"10.1021\/j100058a043","volume":"98","author":"D Sitkoff","year":"1998","unstructured":"Sitkoff D, Sharp KA, Honig B (1998) Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98(7):1978\u20131988","journal-title":"J Phys Chem"},{"key":"20_CR36","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1007\/978-1-61779-465-0_15","volume-title":"Computational drug discovery and design. Methods in molecular biology","author":"S Schneider","year":"2012","unstructured":"Schneider S, Saladin A, Fiorucci S, Pr\u00e9vost C, Zacharias M (2012) ATTRACT and PTools: open sources programs for protein-protein docking. In: Baron R (ed) Computational drug discovery and design. Methods in molecular biology, vol 819. Springer, Heidelberg, pp 221\u2013232"},{"key":"20_CR37","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1186\/1472-6807-9-27","volume":"9","author":"A Saladin","year":"2009","unstructured":"Saladin A, Fiorucci S, Poulain P, Prevost C, Zacharias M (2009) PTools: an opensource molecular docking library. BMC Struct Biol 9:27","journal-title":"BMC Struct Biol"}],"container-title":["Methods in Molecular Biology","Immunoinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-4939-1115-8_20","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,27]],"date-time":"2023-07-27T12:24:35Z","timestamp":1690460675000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-4939-1115-8_20"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014]]},"ISBN":["9781493911141","9781493911158"],"references-count":37,"URL":"https:\/\/doi.org\/10.1007\/978-1-4939-1115-8_20","relation":{"is-part-of":[{"id-type":"doi","id":"https:\/\/doi.org\/10.1007\/978-1-4939-1115-8","asserted-by":"object"}]},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014]]},"assertion":[{"value":"27 June 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}